fix print_only mode and add auto analysis folder

[yongninglei]

1. I fix the problem with print_only mode, basically if there is something in your analysis folder, it will read the existing config files in the analysis folder, not the ones you are pass as input arguments. This means that now the file will be copied in prepare mode to the output folder and when running it will take the config file from the subject output. This way we know exactly what was run.
2. I add one function in prepare file, called prepare_analysis folder, it will auto check if analysis folder exist and it will create a new one if the content inside is different from the input
3. I delete analysis input in config.yaml
4. i rename some parameters in container_specific_configs

[garikoitz]

1./ requirements needs to be fixed (no repetitions, add scipy and bids) 2./ with no arguments, it should provide useful info 3./ it does not use the right singularity version 4./ edit this line: "Please check if the job_script is properlly defined and then starting run_lc", Please check (1) that launchcontainers prepared the data properly, and (2) the command line for each subject is properly formed. The first time you run this, you could even copy and pase the command line to check if everything is working properly, before launching multiple subjects. Once these checks are done, you can just run the same line, adding "--run_lc". 5./ Right now the cmd text is manually generated, it should print out exactly what dask will send to the scheduler 6./ Add check if there is no fmap, then give warning 7./ Add the if RUN=True do things, otherwise don't do anything for that subject